MOSCOW, March 20 (Reuters) - President Vladimir Putin said on Thursday Russian companies must be registered in Russia and have a transparent ownership structure, emphasising one of his main messages that business should be brought back home.

"Russian companies should be registered on the territory of our nation, in our country and have a transparent ownership structure," Putin told heads of Russia's largest companies at a local business conference.

"I am convinced that you are also interested in this."

Russian business owners are worried about the impact of Western sanctions over Putin's move to annex Crimea. The European Union warned of ramping up punitive measures against Russia, including politically sensitive economic sanctions.

The European Union is Russia's top trading partner, accounting for almost half of its exports and imports, according to the latest data from the economy ministry.

Putin promised a "de-offshorisation" push to stem capital flight after returning to the Kremlin in May 2012 for a third presidential term. On Thursday, with Russia facing growing isolation by the West, he repeated his pledge.

"Our task is not only to limit the possibilities of offshore schemes," Putin said on Thursday.

"We understand perfectly well that little can be achieved through prohibitions. The main direction of our work is in something else: it is necessary to increase the attractiveness of the Russian jurisdiction, improve the business climate, and strengthen legal guarantees and the protection of property." (Addditional reporting by Steve Gutterman and Maria Kiselyova; Writing by Lidia Kelly; editing by Elizabeth Piper)